To improve the supervision efficiency and level of water conservancy projects and ensure the realization of project construction and operation goals, based on the review of the supervision work of key small and medium rivers and major water conservancy projects in China, the evaluation indexes of the supervision efficiency of water conservancy projects under construction are established. A comprehensive evaluation model for the evaluation of supervision efficiency of water conservancy projects is established by using the C-OWA operator weighting method and the gray system theory based on the cost-benefit method for reference to take the input and results as the target layer. The rationality and accuracy of the index system are validated through case analysis.